Figure 4.

The reconstruction of an ancestral cluster. (a) Detailed comparison of gene content and order is shown for the four clusters included
in CLIC #39 (see Table 3), containing genes from the OR1 and OR3 families. A schematic
ancestral configuration is shown at the bottom row, with inferred minimal number of
genes. Genes are presented as triangles colored by subfamily affiliation (bottom row;
yellow for subfamily OR1G). Inferred chromosomal rearrangements relative to the ancestor
are specified for each species: circle = insertion, X = deletion, arrow = inversion,
broken line with number of genes = tandem duplication. A complex duplication in rodent
genomes, involving subfamilies OR3A, OR1P, and OR1A, is marked with a rectangle. This
duplication was probably formed via several events, some of which occurred after the
split between mouse and rat lineages. The same region had experienced another independent
event in the dog genome, in which three genes from subfamilies 1A and 1P were inverted
as one unit. Tandem duplication in one end of the rodent clusters forms a series of
numerous adjacent highly similar genes from the same subfamily (OR1J). The human and
mouse orthologous clusters were studied and compared previously [27], and a complex
orthology relationship among the genes was described. (b) A phylogenetic tree of CLIC #39 ORs from which the ancestral cluster gene count can
be inferred. The phylogenetic tree was generated with Mega version 3.1 [58] using
ME algorithm, and Poisson correction for distance calculation. Protein sequences were
aligned with Clustalx [59]. The colors of circles next to the phylogenetic branches
indicate species (blue = dog, green = rat, orange = mouse, red = human). OR51D1 serves
as an out-group. CLIC, clusters in conservation; OR, olfactory receptor.